Topology is a strong global constraint that can be useful in generating geometrically accurate segmentations of anatomical structures. Conversely, topological “defects” or departures from the true topology of a structure due to segmentation errors can greatly reduce the utility of anatomical models. In this chapter we cover methods for integrating topological constraints into segmentation proce...

While modern imaging technologies such as fMRI have opened exciting possibilities for studying the brain in vivo, histological sections remain the best way to study brain anatomy at the level of neurons. The procedure for building histological atlas changed little since 1909 and identifying brain regions is a still a labor intensive process performed only by experienced neuroanatomists. Existin...

This paper presents the main research achievements of the EU Marie Curie RTN project titled 3D Anatomical Human (3DAH) (http://3dah.miralab.ch/). The objective of 3DAH research network is to increase, by scientific exchange, the development of realistic functional 3D models of the human musculoskeletal system, with the methodology demonstrated on the human neuromusculoskeletal system of the low...

Computational musculoskeletal (MSK) models - 3D graphics-based models that accurately simulate the anatomical architecture and/or the biomechanical behaviour of organ systems consisting of skeletal muscles, tendons, ligaments, cartilage and bones - are valued biomedical tools, with applications ranging from pathological diagnosis to surgical planning. However, current MSK models are often limit...

Percutaneous coronary intervention (PCI) of multivessel and/or left main stem disease have been shown to be potentially legitimate revascularization alternatives in appropriately selected patients. Risk stratification is an important component in guiding patients to identify the most appropriate revascularization modality (PCI or coronary artery bypass grafting [CABG]) in conjunction with the H...

We present a system to reconstruct subject-specific anatomy models while relying only on exterior measurements represented by point clouds. Our model combines geometry, kinematics, and skin deformations (skinning). This joint model can be adapted to different individuals without breaking its functionality, i.e., the bones and the skin remain well-articulated after the adaptation. We propose an ...

A primary objective of the eMouseAtlas Project is to enable 3D spatial mapping of whole embryo gene expression data to capture complex 3D patterns for indexing, visualization, cross-comparison and analysis. For this we have developed a spatio-temporal framework based on 3D models of embryos at different stages of development coupled with an anatomical ontology. Here we introduce a method of def...

A detailed model of the shape of anatomical structures can significantly improve the ability to segment such structures from medical images. Statistical models representing the variation of shape and appearance can be constructed from suitably annotated training sets. Such models can be used to synthesize images of anatomy, and to search new images to accurately locate the structures of interes...

Reentry around non-conducting ventricular scar tissue, which often causes lethal arrhythmias, is typically treated by rapid stimulation from an implantable defibrillator. However, the mechanisms of termination (success and failure) are poorly understood. To elucidate such mechanisms, we studied pacing of anatomical reentry in 1-D and 2-D excitable cardiac media models. Our results suggest that ...

Anatomical models are important training and teaching tools in the clinical environment and are routinely used in medical imaging research. Advances in segmentation algorithms and increased availability of three-dimensional (3D) printers have made it possible to create cost-efficient patient-specific models without expert knowledge. We introduce a general workflow that can be used to convert vo...